--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/primer.design.xml	Fri May 19 05:10:09 2017 -0400
@@ -0,0 +1,101 @@
+<tool profile="16.07" id="mothur_primer_design" name="Primer.design" version="@WRAPPER_VERSION@.0">
+    <description>identify sequence fragments that are specific to particular OTUs</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="stdio"/>
+    <expand macro="version_command"/>
+    <command><![CDATA[
+        @SHELL_OPTIONS@
+
+        ## create symlinks to input datasets
+        ln -s "$fasta" fasta.dat &&
+        ln -s "$otu" otu.dat &&
+        ln -s "$name" name.dat &&
+        ln -s "$count" count.dat &&
+
+        echo 'primer.design(
+            fasta=fasta.dat,
+            list=otu.dat,
+            #if $label:
+                label=$label,
+            #end if
+                otulabel=$otulabel,
+            #if $name:
+                name=name.dat,
+            #end if
+            #if $count:
+                count=count.dat,
+            #end if
+            #if $cutoff:
+                cutoff=$cutoff,
+            #end if
+            #if $mintm:
+                mintm=$mintm,
+            #end if
+            #if $maxtm:
+                maxtm=$maxtm,
+            #end if
+            pdiffs=$pdiffs,
+            length=$length,
+            processors='\${GALAXY_SLOTS:-8}'
+        )'
+        | sed 's/ //g'  ## mothur trips over whitespace
+        | mothur
+        | tee mothur.out.log
+    ]]></command>
+    <inputs>
+        <param name="fasta" type="data" format="mothur.align" label="fasta - provide aligned fasta file"/>
+        <param name="otu" type="data" format="mothur.list" label="list - OTU list file"/>
+        <param name="label" type="select" optional="true" multiple="false" label="label - OTU Labels" help="If none selected, the first label in your file will be used">
+            <expand macro="labeloptions"/>
+        </param>
+        <param name="otulabel" type="select" optional="false" multiple="false" label="otulabel - choose an OTU name">
+            <options>
+                <filter type="data_meta" ref="otu" key="otulabels"/>
+            </options>
+        </param>
+        <param name="name" type="data" format="mothur.names" optional="true" label="name - names file associated with your fasta file"/>
+        <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count table associated with your fasta file"/>
+        <param name="pdiffs" type="integer" value="0" min="0" label="pdiffs - specify the number of differences allowed in the primer" help=""/>
+        <param name="length" type="integer" value="18" min="0" label="length - indicate the length of the primer" help=""/>
+        <param name="mintm" type="integer" value="" optional="true" label="mintm - indicate minimum melting temperature" help=""/>
+        <param name="maxtm" type="integer" value="" optional="true" label="maxtm - indicate maximum melting temperature" help=""/>
+        <param name="cutoff" type="integer" value="" optional="true" min="0" max="100" label="cutoff - set a percentage of sequences that support the base" help="For example: cutoff=97 would only return a sequence that only showed ambiguities for bases that were not supported by at least 97% of sequences."/>
+    </inputs>
+    <outputs>
+        <expand macro="logfile-output"/>
+        <data name="fasta_out" format="mothur.align" from_work_dir="otu*.cons.fasta" label="${tool.name} on ${on_string}: cons.fasta"/>
+        <data name="summary_out" format="tabular" from_work_dir="otu*.primer.summary" label="${tool.name} on ${on_string}: primer.summary"/>
+        <data name="list_out" format="mothur.list" from_work_dir="otu*.pick.*" label="${tool.name} on ${on_string}: pick.list"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="fasta" value="amazon.align_head" ftype="mothur.align"/>
+            <param name="otu" value="amazon.align_head.list" ftype="mothur.list"/>
+            <param name="otulabel" value="Otu1"/>
+            <param name="label" value="0.30"/>
+            <output name="fasta_out" md5="a5c8c17814f02124194dba2e37f566c7" ftype="mothur.align"/>
+            <output name="summary_out" md5="8dd341c49c26c6d0f8026b34cb7bc925" ftype="tabular"/>
+            <output name="list_out" md5="0a73804f3d48c668b4dab85c76d2c767" ftype="mothur.list"/>
+            <expand macro="logfile-test"/>
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+
+@MOTHUR_OVERVIEW@
+
+**Command Documentation**
+
+The primer.design_ allows you to identify sequence fragments that are specific to particular OTUs.
+
+.. _primer.design: https://www.mothur.org/wiki/Primer.design
+
+]]>
+    </help>
+    <citations>
+        <citation type="doi">10.1128/AEM.01541-09</citation>
+    </citations>
+</tool>